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CONTRIBUTING.md

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Contributing

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions

Report Bugs

Report bugs at https://github.com/czbiohub/orpheum/issues

If you are reporting a bug, please include:

  • Your operating system name and version.
  • Any details about your local setup that might be helpful in troubleshooting.
  • Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with "bug" is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with "feature" is open to whoever wants to implement it.

Write Documentation

Kmer-hashing tools could always use more documentation, whether as part of the official Kmer-hashing tools docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to file an issue at https://github.com/czbiohub/orpheum/issues

If you are proposing a feature:

  • Explain in detail how it would work.
  • Keep the scope as narrow as possible, to make it easier to implement.
  • Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here's how to set up orpheum for local development.

  1. Fork the orpheum repo on GitHub.

  2. Clone your fork locally:

    $ git clone [email protected]:your_name_here/orpheum.git

  3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

    $ mkvirtualenv orpheum
$ cd orpheum/
$ python setup.py develop

  4. Create a branch for local development:

    $ git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  5. When you're done making changes, format your files with black and check that your code passes the tests, including testing other Python versions with tox:

    $ black . --check    # see reformatting changes that would happen
# black .            # reformat as necessary
$ py.test
$ tox

    To get black and tox, just pip install them into your virtualenv. Note: run formatting commands from the top orpheum directory.

  6. Commit your changes and push your branch to GitHub:

    $ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

  7. Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

  1. The pull request should include tests.
  2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
  3. The pull request should work for Python 3.6 and 3.7. Check https://travis-ci.org/czbiohub/orpheum/pull\_requests and make sure that the tests pass for all supported Python versions.

Tips

To run a subset of tests:

$ python -m unittest tests.test_commandline